BMC Biophysics | Article collections | Biological Diffusion and Brownian Dynamics

Membrane microdomains emergence through non-homogeneous diffusion

Hédi A Soula, Antoine Coulon, Guillaume Beslon BMC Biophysics 2012, 5:6 (30 April 2012)

Abstract | Full text | PDF | PubMed | Editor’s summary

Non-homogeneous diffusion in cell membranes leads to the formation of protein/ lipid enriched microdomains in a model of membrane dynamics, with domains of high viscosity tending to gather a statistically larger proportion of diffusive particles

An upper limit for macromolecular crowding effects

Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface

Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.

Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations

Balaji VS Iyer, Martin Kenward, Gaurav Arya BMC Biophysics 2011, 4:8 (15 April 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Gaurav Arya and colleagues review results from state-of-the-art microscopy and chromosome conformation capture techniques that are being used to understand the three dimensional structure of the genome and the physical principles governing its folding.

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.

Brownian dynamics simulation of analytical ultracentrifugation experiments

AI Díez, A Ortega, J Garcia de la Tore BMC Biophysics 2011, 4:6 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Using Brownian dynamics to simulate the trajectories of the particles could lead to improved and efficient predictions of time-dependent concentration profiles during analytical ultracentrifugation experiments.

A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction

Jorge L Barreda, Huan-Xiang Zhou BMC Biophysics 2011, 4:5 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

An analytical solution to modeling the diffusion and reaction of acetylcholine in a neuromuscular junction and the binding of Ca2+ in a dyadic cleft provides a unique benchmark for testing numerical modeling methods.

Gated Diffusion-controlled Reactions

J Andrew McCammon BMC Biophysics 2011, 4:4 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Andy McCammon discusses both the protein-centric and detailed dynamic simulation methods that have been applied to predict rates of ligand binding and reactivity at protein active sites and the biological implications of these findings.

Diffusion in crowded biological environments: applications of Brownian dynamics

Maciej Długosz, Joanna Trylska BMC Biophysics 2011, 4:3 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.

Diffusion and association processes in biological systems: theory, computation and experiment

Paolo Mereghetti, Daria Kokh, J Andrew McCammon, Rebecca C Wade BMC Biophysics 2011, 4:2 (2 March 2011)

Abstract | Full text | PDF | PubMed | Editor’s summary

Rebecca Wade and colleagues provide a snapshot of research from a thematic series of articles on biological diffusion and Brownian dynamics simulations, which highlights a vibrant research field with growing synergy between experimental and computational studies.

		Research article Membrane microdomains emergence through non-homogeneous diffusion Hédi A Soula, Antoine Coulon, Guillaume Beslon BMC Biophysics 2012, 5:6 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Non-homogeneous diffusion in cell membranes leads to the formation of protein/ lipid enriched microdomains in a model of membrane dynamics, with domains of high viscosity tending to gather a statistically larger proportion of diffusive particles
		Research article An upper limit for macromolecular crowding effects Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
		Research article Diffusion of hydrophobin proteins in solution and interactions with a graphite surface Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
		Review Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations Balaji VS Iyer, Martin Kenward, Gaurav Arya BMC Biophysics 2011, 4:8 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gaurav Arya and colleagues review results from state-of-the-art microscopy and chromosome conformation capture techniques that are being used to understand the three dimensional structure of the genome and the physical principles governing its folding.
		Research article Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.
		Research article Brownian dynamics simulation of analytical ultracentrifugation experiments AI Díez, A Ortega, J Garcia de la Tore BMC Biophysics 2011, 4:6 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using Brownian dynamics to simulate the trajectories of the particles could lead to improved and efficient predictions of time-dependent concentration profiles during analytical ultracentrifugation experiments.
		Research article A solvable model for the diffusion and reaction of neurotransmitters in a synaptic junction Jorge L Barreda, Huan-Xiang Zhou BMC Biophysics 2011, 4:5 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An analytical solution to modeling the diffusion and reaction of acetylcholine in a neuromuscular junction and the binding of Ca2+ in a dyadic cleft provides a unique benchmark for testing numerical modeling methods.
		Review Gated Diffusion-controlled Reactions J Andrew McCammon BMC Biophysics 2011, 4:4 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Andy McCammon discusses both the protein-centric and detailed dynamic simulation methods that have been applied to predict rates of ligand binding and reactivity at protein active sites and the biological implications of these findings.
		Review Diffusion in crowded biological environments: applications of Brownian dynamics Maciej Długosz, Joanna Trylska BMC Biophysics 2011, 4:3 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.
		Editorial Diffusion and association processes in biological systems: theory, computation and experiment Paolo Mereghetti, Daria Kokh, J Andrew McCammon, Rebecca C Wade BMC Biophysics 2011, 4:2 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Rebecca Wade and colleagues provide a snapshot of research from a thematic series of articles on biological diffusion and Brownian dynamics simulations, which highlights a vibrant research field with growing synergy between experimental and computational studies.

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